Note: Intro -- Copyright -- Dedication -- Preface -- Acknowledgments -- Contents -- Contents in Detail -- Special Sections -- Map of the Maps -- Part 1: The Facts of Life -- Chapter 1: Why: Biology by the Numbers -- 1.1 Biological Cartography -- 1.2 Physical Biology of the Cell -- Model Building Requires a Substrate of Biological Facts and Physical (or Chemical) Principles -- 1.3 The Stuff of Life -- Organisms Are Constructed from Four Great Classes of Macromolecules -- Nucleic Acids and Proteins Are Polymer Languages with Different Alphabets -- 1.4 Model Building in Biology -- 1.4.1 Models as Idealizations -- Biological Stuff Can Be Idealized Using Many Different Physical Models -- 1.4.2 Cartoons and Models -- Biological Cartoons Select Those Features of the Problem Thought to Be Essential -- Quantitative Models Can Be Built by Mathematicizing the Cartoons -- 1.5 Quantitative Models and the Power of Idealization -- 1.5.1 On the Springiness of Stuff -- 1.5.2 The Toolbox of Fundamental Physical Models -- 1.5.3 The Unifying Ideas of Biology -- 1.5.4 Mathematical Toolkit -- 1.5.5 The Role of Estimates -- 1.5.6 On Being Wrong -- 1.5.7 Rules of Thumb: Biology by the Numbers -- 1.6 Summary and Conclusions -- 1.7 Further Reading -- 1.8 References -- Chapter 2: What and Where: Construction Plans for Cells and Organisms -- 2.1 An Ode to E. coli -- 2.1.1 The Bacterial Standard Ruler -- The Bacterium E. coli Will Serve as Our Standard Ruler -- 2.1.2 Taking the Molecular Census -- The Cellular Interior Is Highly Crowded, with Mean Spacings Between Molecules That Are Comparable to Molecular Dimensions -- 2.1.3 Looking Inside Cells -- 2.1.4 Where Does E. coli Fit? -- Biological Structures Exist Over a Huge Range of Scales -- 2.2 Cells and Structures within Them -- 2.2.1 Cells: A Rogue's Gallery. , Cells Come in a Wide Variety of Shapes and Sizes and with a Huge Range of Functions -- Cells from Humans Have a Huge Diversity of Structure and Function -- 2.2.2 The Cellular Interior: Organelles -- 2.2.3 Macromolecular Assemblies: The Whole is Greater than the Sum of the Parts -- Macromolecules Come Together to Form Assemblies -- Helical Motifs Are Seen Repeatedly in Molecular Assemblies -- Macromolecular Assemblies Are Arranged in Superstructures -- 2.2.4 Viruses as Assemblies -- 2.2.5 The Molecular Architecture of Cells: From Protein Data Bank (PDB) Files to Ribbon Diagrams -- Macromolecular Structure Is Characterized Fundamentally by Atomic Coordinates -- Chemical Groups Allow Us to Classify Parts of the Structure of Macromolecules -- 2.3 Telescoping Up in Scale: Cells Don't Go It Alone -- 2.3.1 Multicellularity as One of Evolution's Great Inventions -- Teaming Up in a Crisis: Lifestyle of Dictyostelium discoideum -- Multicellular Organisms Have Many Distinct Communities of Cells -- 2.3.2 Cellular Structures from Tissues to Nerve Networks -- One Class of Multicellular Structures is the Epithelial Sheets -- Tissues Are Collections of Cells and Extracellular Matrix -- Nerve Cells Form Complex, Multicellular Complexes -- 2.3.3 Multicellular Organisms -- Cells Differentiate During Development Leading to Entire Organisms -- The Cells of the Nematode Worm, Caenorhabditis Elegans, Have Been Charted, Yielding a Cell-by-Cell Picture of the Organism -- Higher-Level Structures Exist as Colonies of Organisms -- 2.4 Summary and Conclusions -- 2.5 Problems -- 2.6 Further Reading -- 2.7 References -- Chapter 3: When: Stopwatches at Many Scales -- 3.1 The Hierarchy of Temporal Scales -- 3.1.1 The Pageant of Biological Processes -- Biological Processes Are Characterized by a Huge Diversity of Time Scales -- 3.1.2 The Evolutionary Stopwatch. , 3.1.3 The Cell Cycle and the Standard Clock -- The E. coli Cell Cycle Will Serve as Our Standard Stopwatch -- 3.1.4 Three Views of Time in Biology -- 3.2 Procedural Time -- 3.2.1 The Machines (or Processes) of the Central Dogma -- The Central Dogma Describes the Processes Whereby the Genetic Information Is Expressed Chemically -- The Processes of the Central Dogma Are Carried Out by Sophisticated Molecular Machines -- 3.2.2 Clocks and Oscillators -- Developing Embryos Divide on a Regular Schedule Dictated by an Internal Clock -- Diurnal Clocks Allow Cells and Organisms to Be on Time Everyday -- 3.3 Relative Time -- 3.3.1 Checkpoints and the Cell Cycle -- The Eukaryotic Cell Cycle Consists of Four Phases Involving Molecular Synthesis and Organization -- 3.3.2 Measuring Relative Time -- Genetic Networks Are Collections of Genes Whose Expression Is Interrelated -- The Formation of the Bacterial Flagellum Is Intricately Organized in Space and Time -- 3.3.3 Killing the Cell: The Life Cycles of Viruses -- Viral Life Cycles Include a Series of Self-Assembly Processes -- 3.3.4 The Process of Development -- 3.4 Manipulated Time -- 3.4.1 Chemical Kinetics and Enzyme Turnover -- 3.4.2 Beating the Diffusive Speed Limit -- Diffusion Is the Random Motion of Microscopic Particles in Solution -- Diffusion Times Depend upon the Length Scale -- Diffusive Transport at the Synaptic Junction Is the Dynamical Mechanism for Neuronal Communication -- Molecular Motors Move Cargo over Large Distances in a Directed Way -- Membrane-Bound Proteins Transport Molecules from One Side of a Membrane to the Other -- 3.4.3 Beating the Replication Limit -- 3.4.4 Eggs and Spores: Planning for the Next Generation -- 3.5 Summary and Conclusions -- 3.6 Problems -- 3.7 Further Reading -- 3.8 References -- Chapter 4: Who: "Bless the Little Beasties" -- 4.1 Choosing a Grain of Sand. , Modern Genetics Began with the Use of Peas as a Model System -- 4.1.1 Biochemistry and Genetics -- 4.2 Hemoglobin as a Model Protein -- 4.2.1 Hemoglobin, Receptor-Ligand Binding, and the Other Bohr -- The Binding of Oxygen to Hemoglobin Has Served as a Model System for Ligand-Receptor Interactions More Generally -- Quantitative Analysis of Hemoglobin Is Based upon Measuring the Fractional Occupancy of the Oxygen-Binding Sites as a Function o -- 4.2.2 Hemoglobin and the Origins of Structural Biology -- The Study of the Mass of Hemoglobin Was Central in the Development of Centrifugation -- Structural Biology Has Its Roots in the Determination of the Structure of Hemoglobin -- 4.2.3 Hemoglobin and Molecular Models of Disease -- 4.2.4 The Rise of Allostery and Cooperativity -- 4.3 Bacteriophages and Molecular Biology -- 4.3.1 Bacteriophages and the Origins of Molecular Biology -- Bacteriophages Have Sometimes Been Called the "Hydrogen Atoms of Biology" -- Experiments on Phages and Their Bacterial Hosts Demonstrated That Natural Selection Is Operative in Microscopic Organisms -- The Hershey-Chase Experiment Both Confirmed the Nature of Genetic Material and Elucidated One of the Mechanisms of Viral DNA Ent -- Experiments on Phage T4 Demonstrated the Sequence Hypothesis of Collinearity of DNA and Proteins -- The Triplet Nature of the Genetic Code and DNA Sequencing Were Carried Out on Phage Systems -- Phages Were Instrumental in Elucidating the Existence of mRNA -- General Ideas about Gene Regulation Were Learned from the Study of Viruses as a Model System -- 4.3.2 Bacteriophages and Modern Biophysics -- Many Single-Molecule Studies of Molecular Motors Have Been Performed on Motors from Bacteriophages -- 4.4 A Tale of Two Cells: E. coli As a Model System -- 4.4.1 Bacteria and Molecular Biology -- 4.4.2 E. coli and the Central Dogma. , The Hypothesis of Conservative Replication Has Falsifiable Consequences -- Extracts from E. coli Were Used to Perform In Vitro Synthesis of DNA, mRNA, and Proteins -- 4.4.3 The lac Operon as the "Hydrogen Atom" of Genetic Circuits -- Gene Regulation in E. coli Serves as a Model for Genetic Circuits in General -- The lac Operon Is a Genetic Network That Controls the Production of the Enzymes Responsible for Digesting the Sugar Lactose -- 4.4.4 Signaling and Motility: The Case of Bacterial Chemotaxis -- E. coli Has Served as a Model System for the Analysis of Cell Motility -- 4.5 Yeast: From Biochemistry to the Cell Cycle -- Yeast Has Served as a Model System Leading to Insights in Contexts Ranging from Vitalism to the Functioning of Enzymes to Eukary -- 4.5.1 Yeast and the Rise of Biochemistry -- 4.5.2 Dissecting the Cell Cycle -- 4.5.3 Deciding Which Way Is Up: Yeast and Polarity -- 4.5.4 Dissecting Membrane Traffic -- 4.5.5 Genomics and Proteomics -- 4.6 Flies and Modern Biology -- 4.6.1 Flies and the Rise of Modern Genetics -- Drosophila melanogaster Has Served as a Model System for Studies Ranging from Genetics to Development to the Functioning of the Brain and Even Behavior -- 4.6.2 How the Fly Got His Stripes -- 4.7 Of Mice and Men -- 4.8 The Case for Exotica -- 4.8.1 Specialists and Experts -- 4.8.2 The Squid Giant Axon and Biological Electricity -- There Is a Steady-State Potential Difference Across the Membrane of Nerve Cells -- Nerve Cells Propagate Electrical Signals and Use Them to Communicate with Each Other -- 4.8.3 Exotica Toolkit -- 4.9 Summary and Conclusions -- 4.10 Problems -- 4.11 Further reading -- 4.12 References -- Part 2: Life at Rest -- Chapter 5: Mechanical and Chemical Equilibrium in the Living Cell -- 5.1 Energy and the Life of Cells -- 5.1.1 The Interplay of Deterministic and Thermal Forces. , Thermal Jostling of Particles Must Be Accounted for in Biological Systems.